Volume 18, Issue 3, Pages 354-365 (March 2010) ATP-Induced Conformational Dynamics in the AAA+ Motor Unit of Magnesium Chelatase  Joakim Lundqvist, Hans Elmlund, Ragna Peterson Wulff, Lisa Berglund, Dominika Elmlund, Cecilia Emanuelsson, Hans Hebert, Robert D. Willows, Mats Hansson, Martin Lindahl, Salam Al-Karadaghi  Structure  Volume 18, Issue 3, Pages 354-365 (March 2010) DOI: 10.1016/j.str.2010.01.001 Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 1 Sequence and Fold Comparison of Subunits BchI and BchD of Magnesium Chelatase (A) Structure-based alignment of the amino acid sequences of subunit BchI and the AAA+ module of BchD. Secondary structure elements of the BchI subunit (PDB code 1G8P) are shown on top of the alignment (arrows: strands; spirals: α helices). The coloring of secondary structure elements follows the topology diagrams in (B) and (C). The numbering of secondary structure elements follows the convention for AAA+ proteins (Erzberger and Berger, 2006; Iyer et al., 2004). The positions of characteristic AAA+ motifs are also marked along the sequence: Walker A and B motifs (W-A and W-B), pre-sensor I insert (PS-I), helix 2 insert (H2-insert), the arginine finger (ARG-finger), and sensor 1 and 2 (S-1 and S-2). The residues identified in the crosslinking study to crosslink to the integrin I domain of subunit BchD are marked with asterisks (Lys 16 and Lys 130 and Lys133 from the H2 insert). RHOCA, Rhodobacter capsulatus; CHLVI, Chlorobium vibrioforme; SYNY3, Synechocystis sp.; Tobac, Nicotiana tabacum. (B) Topology diagram of subunit BchD constructed according to the homology model guided by the structure-based sequence alignment shown in (A) and built using the X-ray crystallographic structure of subunit BchI as a modeling template. (C) Topology diagram of the BchI subunit. (D) Theoretical simulations were used to verify the possible position of the helical bundle domain of subunit BchD in relation to the AAA+ core domain. The simulations show minimum energy solutions that fit the arrangement used for building the trimer around the three-fold axis of the complex shown in Figure 4. Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 2 Stereo View of the Reconstructed Model of the ID Complex in the Presence of ADP at 7.5 Å Resolution (A) The ID complex from the top showing the BchD ring (gold). (B) The ID complex showing the bottom part which was assigned to the BchI ring (gray). (C) Side view of the ID complex showing the suggested C-terminal integrin I domain and the proline-rich and acidic residue-rich regions (green and orange) of the BchD dimer. Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 3 The Location of Amino Acid Residues Identified to Crosslink to Each Other (A) Table showing the crosslinked BchI and BchD residues and the approximate distances between them (see also Table S1). (B) Overall view of the reconstruction with the integrin I domains docked into the density according to the position identified by the crosslinking study. (C, D) Details of the structure in the crosslinked region are shown. The crosslinked residues are shown as space-filling spheres and are color-coded according to the table in (A). (E) A stereo view showing the quality of fit of the integrin I domains into the reconstruction density. The region shown is the same as in Figure 2C. Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 4 The Density Remaining after the Docking of the Integrin I Domain (A) Side view of the ID complex. The central top part (blue) is thought to represent the density for the AAA+ modules of BchD, while green and brown mark the density for proline and acidic residues rich domains belonging to different BchD monomers (see also Figure 2C). The ribbon models represent the integrin I domains (green and brown) and the BchI ring (gray). (B) Top view of the ID complex showing the tentative density of the BchD AAA+ module trimer. (C) Docking of the homology model of BchD AAA+ module into the density. Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 5 The BchI:BchD Complex of Magnesium Chelatase in Different Nucleotide States (A–C) Top (A), side (B), and bottom (C) views of the complex in the presence of ADP, filtered to 13 Å resolution for the comparison with the other reconstructions (see also Figure S1). (D–F) Top (D), side (E), and bottom (F) views of the complex in the presence of the nonhydrolyzable ATP analog AMPPNP. (G–I) Top (G), side (H), and bottom (I) views of the complex in the presence of ATP. (J–L) The corresponding views of the complex between subunits CobS:CobT of the homologs cobaltochelatase in the presence of ATP (Lundqvist et al., 2009). Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 6 Difference Density Highlighting the Regions with the Largest Shifts in Conformation during the Transition between the ADP and AMPPNP States of the ID Complex (Red) These are concentrated to the top of the BchD-ring, to the middle region (which was assigned to the integrin I domains) and to some parts of the BchI ring (bottom part). Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 7 The Putative ATP-Binding Site between Monomers in a BchI Homodimer (A) The BchI ring with the X-ray crystallographic structure of BchI docked into it. The ATP molecule is shown in space-filling representation (green). (B) An ATP molecule (shown in sticks representation) was placed between two monomers after superposition of the BchI ring with the HslU ring. The positions of the characteristic functional residues are marked (R-F: the arginine finger; S-II: sensor II; W-A and W-B: Walker A and Walker B motifs). (C) Schematic presentation of the conformational cycle involving the integrin I domains changing their positions relative to the BchI ring and the monomers within the BchI ring changing interaction partners (a transition from black:black-white:white dimers to black:white dimers). Structure 2010 18, 354-365DOI: (10.1016/j.str.2010.01.001) Copyright © 2010 Elsevier Ltd Terms and Conditions